Search results for the GEO ID: GSE12086  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM305047 | GPL570 |
|
lymphoblast_RPfamily1_003-116
|
Lymphoblast cell line from transformed lymphocytes.
|
human_female_recessive retinitis pigmentosa_transformed lymphocyte
|
n/a
|
| Sample_geo_accession | GSM305047
| | Sample_status | Public on Jul 14 2008
| | Sample_submission_date | Jul 11 2008
| | Sample_last_update_date | Jul 14 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | none
| | Sample_growth_protocol_ch1 | Lymphoblasts were immortalized and grown at the Harvard Partners Center for Genetics and Genomics. Prior to harvesting for mRNA isolation, cells were grown to confluence in T25 flasks (10 ml media/flask), and then transferred to T75 flasks with an additional 15 ml of fresh media. When the cells reached confluence (typically after 3 - 6 weeks), another 25 ml of media was added, for a total of 50 ml. The cells were harvested 24 hours after adding media.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Harvested lymphoblast cell lines were pelleted by centrifugation at 1200 RPM at room temperature and washed twice with PBS buffer and repelleted. Cell pellet was suspended in 2 ml of Trizol, divided into 4 aliquots, and kept at -80 C. An aliquot of the lymphoblast-Trizol suspension was thawed and RNA was purified using the Promega SV Total RNA Isolation kit and resuspended in RNAse-free water.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was labeled at the Dana Farber Cancer Institute Microarray Core Facility using their standard protocol detailed below. 1. RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. 2. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. 3. The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. 4. The purified cRNA is fragmented in order to facilitate the subsequent hybridization step.
| | Sample_hyb_protocol | RNA was further processed at the Dana Farber Cancer Institute Microarray Core Facility using their standard protocol detailed below. 1. The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. 2. The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE. 3. Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.
| | Sample_scan_protocol | Affymetrix Microarray Suite 5.0 was used as scanning software. The target mRNA from the cell sample of interest is fragmented, fluorescently labeled, and washed over the array. Ideally, the components of the target mRNA sample will specifically hybridize to the intended PM strand. The MM strand serves as a control for non-specific cross-hybridization. The fluorescence levels at each PM and MM are then measured using a scanning microscope. MAS software outputs detected fluorescence levels at each probe. When the scanning microscope reads fluorescence activity, it dissects each probe cell (that is, each individual PM and MM cell) into a 6x6 square of pixels, and records the fluorescence levels at each pixel in a file with extension .DAT. To summarize the fluorescence at each cell, MAS ignores the 20 border pixels and returns the 75th percentile fluorescence level of the remaining 16 pixels as the Average Intensity of the probe cell, and records these values in the .CEL file.
| | Sample_data_processing | Raw data reflecting hybridization intensities, from individual probes of 25 different chips were provided as Microarray Suite (MAS) 5.0 experiment data files: .CHP, .TXT, .RPT, .EXP, .CEL (the .TXT and .CEL files are linked below as supplementary files), and were normalised using d-Chip. Background information is provided on the website: http://biosun1.harvard.edu/complab/dchip/normalizing%20arrays.htm The normalized data were extracted into a Microsoft Excel file and hybridization intensities from all probes of the affected patients in individual families were compared to all of the other samples. Significance in multiplex families was tested using a one-tailed Student’s t-test assuming unequal variance, a Bonferroni correction and P-value < 0.05. In families with only one available patient, the transcript in that patient had to have a hybridization signal more than two standard deviations below the mean hybridization intensity in all other patients.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Dyonne,T.,Hartong
| | Sample_contact_email | d.t.hartong@ohk.umcg.nl
| | Sample_contact_laboratory | Ocular Molecular Genetics Institute
| | Sample_contact_department | Massachusetts Eye and Ear Infirmary
| | Sample_contact_institute | Harvard Medical School
| | Sample_contact_address | 243 Charles Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | MA 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305047/suppl/GSM305047.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305047/suppl/GSM305047.txt.gz
| | Sample_series_id | GSE12086
| | Sample_data_row_count | 54613
| | |
|
GSM305048 | GPL570 |
|
lymphoblast_RPfamily1_218-237
|
Lymphoblast cell line from transformed lymphocytes.
|
human_female_recessive retinitis pigmentosa_transformed lymphocyte
|
n/a
|
| Sample_geo_accession | GSM305048
| | Sample_status | Public on Jul 14 2008
| | Sample_submission_date | Jul 11 2008
| | Sample_last_update_date | Jul 14 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | none
| | Sample_growth_protocol_ch1 | Lymphoblasts were immortalized and grown at the Harvard Partners Center for Genetics and Genomics. Prior to harvesting for mRNA isolation, cells were grown to confluence in T25 flasks (10 ml media/flask), and then transferred to T75 flasks with an additional 15 ml of fresh media. When the cells reached confluence (typically after 3 - 6 weeks), another 25 ml of media was added, for a total of 50 ml. The cells were harvested 24 hours after adding media.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Harvested lymphoblast cell lines were pelleted by centrifugation at 1200 RPM at room temperature and washed twice with PBS buffer and repelleted. Cell pellet was suspended in 2 ml of Trizol, divided into 4 aliquots, and kept at -80 C. An aliquot of the lymphoblast-Trizol suspension was thawed and RNA was purified using the Promega SV Total RNA Isolation kit and resuspended in RNAse-free water.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was labeled at the Dana Farber Cancer Institute Microarray Core Facility using their standard protocol detailed below. 1. RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. 2. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. 3. The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. 4. The purified cRNA is fragmented in order to facilitate the subsequent hybridization step.
| | Sample_hyb_protocol | RNA was further processed at the Dana Farber Cancer Institute Microarray Core Facility using their standard protocol detailed below. 1. The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. 2. The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE. 3. Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.
| | Sample_scan_protocol | Affymetrix Microarray Suite 5.0 was used as scanning software. The target mRNA from the cell sample of interest is fragmented, fluorescently labeled, and washed over the array. Ideally, the components of the target mRNA sample will specifically hybridize to the intended PM strand. The MM strand serves as a control for non-specific cross-hybridization. The fluorescence levels at each PM and MM are then measured using a scanning microscope. MAS software outputs detected fluorescence levels at each probe. When the scanning microscope reads fluorescence activity, it dissects each probe cell (that is, each individual PM and MM cell) into a 6x6 square of pixels, and records the fluorescence levels at each pixel in a file with extension .DAT. To summarize the fluorescence at each cell, MAS ignores the 20 border pixels and returns the 75th percentile fluorescence level of the remaining 16 pixels as the Average Intensity of the probe cell, and records these values in the .CEL file.
| | Sample_data_processing | Raw data reflecting hybridization intensities, from individual probes of 25 different chips were provided as Microarray Suite (MAS) 5.0 experiment data files: .CHP, .TXT, .RPT, .EXP, .CEL (the .TXT and .CEL files are linked below as supplementary files), and were normalised using d-Chip. Background information is provided on the website: http://biosun1.harvard.edu/complab/dchip/normalizing%20arrays.htm The normalized data were extracted into a Microsoft Excel file and hybridization intensities from all probes of the affected patients in individual families were compared to all of the other samples. Significance in multiplex families was tested using a one-tailed Student’s t-test assuming unequal variance, a Bonferroni correction and P-value < 0.05. In families with only one available patient, the transcript in that patient had to have a hybridization signal more than two standard deviations below the mean hybridization intensity in all other patients.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Dyonne,T.,Hartong
| | Sample_contact_email | d.t.hartong@ohk.umcg.nl
| | Sample_contact_laboratory | Ocular Molecular Genetics Institute
| | Sample_contact_department | Massachusetts Eye and Ear Infirmary
| | Sample_contact_institute | Harvard Medical School
| | Sample_contact_address | 243 Charles Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | MA 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305048/suppl/GSM305048.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305048/suppl/GSM305048.TXT.gz
| | Sample_series_id | GSE12086
| | Sample_data_row_count | 54613
| | |
|
GSM305049 | GPL570 |
|
lymphoblast_RPfamily_2_003-166
|
Lymphoblast cell line from transformed lymphocytes.
|
human_male_recessive retinitis pigmentosa_transformed lymphocyte
|
n/a
|
| Sample_geo_accession | GSM305049
| | Sample_status | Public on Jul 14 2008
| | Sample_submission_date | Jul 11 2008
| | Sample_last_update_date | Jul 14 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | none
| | Sample_growth_protocol_ch1 | Lymphoblasts were immortalized and grown at the Harvard Partners Center for Genetics and Genomics. Prior to harvesting for mRNA isolation, cells were grown to confluence in T25 flasks (10 ml media/flask), and then transferred to T75 flasks with an additional 15 ml of fresh media. When the cells reached confluence (typically after 3 - 6 weeks), another 25 ml of media was added, for a total of 50 ml. The cells were harvested 24 hours after adding media.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Harvested lymphoblast cell lines were pelleted by centrifugation at 1200 RPM at room temperature and washed twice with PBS buffer and repelleted. Cell pellet was suspended in 2 ml of Trizol, divided into 4 aliquots, and kept at -80 C. An aliquot of the lymphoblast-Trizol suspension was thawed and RNA was purified using the Promega SV Total RNA Isolation kit and resuspended in RNAse-free water.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was labeled at the Dana Farber Cancer Institute Microarray Core Facility using their standard protocol detailed below. 1. RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. 2. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. 3. The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. 4. The purified cRNA is fragmented in order to facilitate the subsequent hybridization step.
| | Sample_hyb_protocol | RNA was further processed at the Dana Farber Cancer Institute Microarray Core Facility using their standard protocol detailed below. 1. The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. 2. The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE. 3. Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.
| | Sample_scan_protocol | Affymetrix Microarray Suite 5.0 was used as scanning software. The target mRNA from the cell sample of interest is fragmented, fluorescently labeled, and washed over the array. Ideally, the components of the target mRNA sample will specifically hybridize to the intended PM strand. The MM strand serves as a control for non-specific cross-hybridization. The fluorescence levels at each PM and MM are then measured using a scanning microscope. MAS software outputs detected fluorescence levels at each probe. When the scanning microscope reads fluorescence activity, it dissects each probe cell (that is, each individual PM and MM cell) into a 6x6 square of pixels, and records the fluorescence levels at each pixel in a file with extension .DAT. To summarize the fluorescence at each cell, MAS ignores the 20 border pixels and returns the 75th percentile fluorescence level of the remaining 16 pixels as the Average Intensity of the probe cell, and records these values in the .CEL file.
| | Sample_data_processing | Raw data reflecting hybridization intensities, from individual probes of 25 different chips were provided as Microarray Suite (MAS) 5.0 experiment data files: .CHP, .TXT, .RPT, .EXP, .CEL (the .TXT and .CEL files are linked below as supplementary files), and were normalised using d-Chip. Background information is provided on the website: http://biosun1.harvard.edu/complab/dchip/normalizing%20arrays.htm The normalized data were extracted into a Microsoft Excel file and hybridization intensities from all probes of the affected patients in individual families were compared to all of the other samples. Significance in multiplex families was tested using a one-tailed Student’s t-test assuming unequal variance, a Bonferroni correction and P-value < 0.05. In families with only one available patient, the transcript in that patient had to have a hybridization signal more than two standard deviations below the mean hybridization intensity in all other patients.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Dyonne,T.,Hartong
| | Sample_contact_email | d.t.hartong@ohk.umcg.nl
| | Sample_contact_laboratory | Ocular Molecular Genetics Institute
| | Sample_contact_department | Massachusetts Eye and Ear Infirmary
| | Sample_contact_institute | Harvard Medical School
| | Sample_contact_address | 243 Charles Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | MA 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305049/suppl/GSM305049.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305049/suppl/GSM305049.TXT.gz
| | Sample_series_id | GSE12086
| | Sample_data_row_count | 54613
| | |
|
GSM305050 | GPL570 |
|
lymphoblast_RPfamily_2_218-304
|
Lymphoblast cell line from transformed lymphocytes.
|
human_male_recessive retinitis pigmentosa_transformed lymphocyte
|
n/a
|
| Sample_geo_accession | GSM305050
| | Sample_status | Public on Jul 14 2008
| | Sample_submission_date | Jul 11 2008
| | Sample_last_update_date | Jul 14 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | none
| | Sample_growth_protocol_ch1 | Lymphoblasts were immortalized and grown at the Harvard Partners Center for Genetics and Genomics. Prior to harvesting for mRNA isolation, cells were grown to confluence in T25 flasks (10 ml media/flask), and then transferred to T75 flasks with an additional 15 ml of fresh media. When the cells reached confluence (typically after 3 - 6 weeks), another 25 ml of media was added, for a total of 50 ml. The cells were harvested 24 hours after adding media.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Harvested lymphoblast cell lines were pelleted by centrifugation at 1200 RPM at room temperature and washed twice with PBS buffer and repelleted. Cell pellet was suspended in 2 ml of Trizol, divided into 4 aliquots, and kept at -80 C. An aliquot of the lymphoblast-Trizol suspension was thawed and RNA was purified using the Promega SV Total RNA Isolation kit and resuspended in RNAse-free water.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was labeled at the Dana Farber Cancer Institute Microarray Core Facility using their standard protocol detailed below. 1. RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. 2. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. 3. The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. 4. The purified cRNA is fragmented in order to facilitate the subsequent hybridization step.
| | Sample_hyb_protocol | RNA was further processed at the Dana Farber Cancer Institute Microarray Core Facility using their standard protocol detailed below. 1. The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. 2. The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE. 3. Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.
| | Sample_scan_protocol | Affymetrix Microarray Suite 5.0 was used as scanning software. The target mRNA from the cell sample of interest is fragmented, fluorescently labeled, and washed over the array. Ideally, the components of the target mRNA sample will specifically hybridize to the intended PM strand. The MM strand serves as a control for non-specific cross-hybridization. The fluorescence levels at each PM and MM are then measured using a scanning microscope. MAS software outputs detected fluorescence levels at each probe. When the scanning microscope reads fluorescence activity, it dissects each probe cell (that is, each individual PM and MM cell) into a 6x6 square of pixels, and records the fluorescence levels at each pixel in a file with extension .DAT. To summarize the fluorescence at each cell, MAS ignores the 20 border pixels and returns the 75th percentile fluorescence level of the remaining 16 pixels as the Average Intensity of the probe cell, and records these values in the .CEL file.
| | Sample_data_processing | Raw data reflecting hybridization intensities, from individual probes of 25 different chips were provided as Microarray Suite (MAS) 5.0 experiment data files: .CHP, .TXT, .RPT, .EXP, .CEL (the .TXT and .CEL files are linked below as supplementary files), and were normalised using d-Chip. Background information is provided on the website: http://biosun1.harvard.edu/complab/dchip/normalizing%20arrays.htm The normalized data were extracted into a Microsoft Excel file and hybridization intensities from all probes of the affected patients in individual families were compared to all of the other samples. Significance in multiplex families was tested using a one-tailed Student’s t-test assuming unequal variance, a Bonferroni correction and P-value < 0.05. In families with only one available patient, the transcript in that patient had to have a hybridization signal more than two standard deviations below the mean hybridization intensity in all other patients.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Dyonne,T.,Hartong
| | Sample_contact_email | d.t.hartong@ohk.umcg.nl
| | Sample_contact_laboratory | Ocular Molecular Genetics Institute
| | Sample_contact_department | Massachusetts Eye and Ear Infirmary
| | Sample_contact_institute | Harvard Medical School
| | Sample_contact_address | 243 Charles Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | MA 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305050/suppl/GSM305050.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305050/suppl/GSM305050.TXT.gz
| | Sample_series_id | GSE12086
| | Sample_data_row_count | 54613
| | |
|
GSM305051 | GPL570 |
|
lymphoblast_RPfamily_3_003-174
|
Lymphoblast cell line from transformed lymphocytes.
|
human_female_recessive retinitis pigmentosa_transformed lymphocyte
|
n/a
|
| Sample_geo_accession | GSM305051
| | Sample_status | Public on Jul 14 2008
| | Sample_submission_date | Jul 11 2008
| | Sample_last_update_date | Jul 14 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | none
| | Sample_growth_protocol_ch1 | Lymphoblasts were immortalized and grown at the Harvard Partners Center for Genetics and Genomics. Prior to harvesting for mRNA isolation, cells were grown to confluence in T25 flasks (10 ml media/flask), and then transferred to T75 flasks with an additional 15 ml of fresh media. When the cells reached confluence (typically after 3 - 6 weeks), another 25 ml of media was added, for a total of 50 ml. The cells were harvested 24 hours after adding media.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Harvested lymphoblast cell lines were pelleted by centrifugation at 1200 RPM at room temperature and washed twice with PBS buffer and repelleted. Cell pellet was suspended in 2 ml of Trizol, divided into 4 aliquots, and kept at -80 C. An aliquot of the lymphoblast-Trizol suspension was thawed and RNA was purified using the Promega SV Total RNA Isolation kit and resuspended in RNAse-free water.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was labeled at the Dana Farber Cancer Institute Microarray Core Facility using their standard protocol detailed below. 1. RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. 2. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. 3. The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. 4. The purified cRNA is fragmented in order to facilitate the subsequent hybridization step.
| | Sample_hyb_protocol | RNA was further processed at the Dana Farber Cancer Institute Microarray Core Facility using their standard protocol detailed below. 1. The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. 2. The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE. 3. Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.
| | Sample_scan_protocol | Affymetrix Microarray Suite 5.0 was used as scanning software. The target mRNA from the cell sample of interest is fragmented, fluorescently labeled, and washed over the array. Ideally, the components of the target mRNA sample will specifically hybridize to the intended PM strand. The MM strand serves as a control for non-specific cross-hybridization. The fluorescence levels at each PM and MM are then measured using a scanning microscope. MAS software outputs detected fluorescence levels at each probe. When the scanning microscope reads fluorescence activity, it dissects each probe cell (that is, each individual PM and MM cell) into a 6x6 square of pixels, and records the fluorescence levels at each pixel in a file with extension .DAT. To summarize the fluorescence at each cell, MAS ignores the 20 border pixels and returns the 75th percentile fluorescence level of the remaining 16 pixels as the Average Intensity of the probe cell, and records these values in the .CEL file.
| | Sample_data_processing | Raw data reflecting hybridization intensities, from individual probes of 25 different chips were provided as Microarray Suite (MAS) 5.0 experiment data files: .CHP, .TXT, .RPT, .EXP, .CEL (the .TXT and .CEL files are linked below as supplementary files), and were normalised using d-Chip. Background information is provided on the website: http://biosun1.harvard.edu/complab/dchip/normalizing%20arrays.htm The normalized data were extracted into a Microsoft Excel file and hybridization intensities from all probes of the affected patients in individual families were compared to all of the other samples. Significance in multiplex families was tested using a one-tailed Student’s t-test assuming unequal variance, a Bonferroni correction and P-value < 0.05. In families with only one available patient, the transcript in that patient had to have a hybridization signal more than two standard deviations below the mean hybridization intensity in all other patients.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Dyonne,T.,Hartong
| | Sample_contact_email | d.t.hartong@ohk.umcg.nl
| | Sample_contact_laboratory | Ocular Molecular Genetics Institute
| | Sample_contact_department | Massachusetts Eye and Ear Infirmary
| | Sample_contact_institute | Harvard Medical School
| | Sample_contact_address | 243 Charles Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | MA 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305051/suppl/GSM305051.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305051/suppl/GSM305051.TXT.gz
| | Sample_series_id | GSE12086
| | Sample_data_row_count | 54613
| | |
|
GSM305052 | GPL570 |
|
lymphoblast_RPfamily_3_003-175
|
Lymphoblast cell line from transformed lymphocytes.
|
human_female_recessive retinitis pigmentosa_transformed lymphocyte
|
n/a
|
| Sample_geo_accession | GSM305052
| | Sample_status | Public on Jul 14 2008
| | Sample_submission_date | Jul 11 2008
| | Sample_last_update_date | Jul 14 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | none
| | Sample_growth_protocol_ch1 | Lymphoblasts were immortalized and grown at the Harvard Partners Center for Genetics and Genomics. Prior to harvesting for mRNA isolation, cells were grown to confluence in T25 flasks (10 ml media/flask), and then transferred to T75 flasks with an additional 15 ml of fresh media. When the cells reached confluence (typically after 3 - 6 weeks), another 25 ml of media was added, for a total of 50 ml. The cells were harvested 24 hours after adding media.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Harvested lymphoblast cell lines were pelleted by centrifugation at 1200 RPM at room temperature and washed twice with PBS buffer and repelleted. Cell pellet was suspended in 2 ml of Trizol, divided into 4 aliquots, and kept at -80 C. An aliquot of the lymphoblast-Trizol suspension was thawed and RNA was purified using the Promega SV Total RNA Isolation kit and resuspended in RNAse-free water.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was labeled at the Dana Farber Cancer Institute Microarray Core Facility using their standard protocol detailed below. 1. RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. 2. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. 3. The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. 4. The purified cRNA is fragmented in order to facilitate the subsequent hybridization step.
| | Sample_hyb_protocol | RNA was further processed at the Dana Farber Cancer Institute Microarray Core Facility using their standard protocol detailed below. 1. The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. 2. The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE. 3. Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.
| | Sample_scan_protocol | Affymetrix Microarray Suite 5.0 was used as scanning software. The target mRNA from the cell sample of interest is fragmented, fluorescently labeled, and washed over the array. Ideally, the components of the target mRNA sample will specifically hybridize to the intended PM strand. The MM strand serves as a control for non-specific cross-hybridization. The fluorescence levels at each PM and MM are then measured using a scanning microscope. MAS software outputs detected fluorescence levels at each probe. When the scanning microscope reads fluorescence activity, it dissects each probe cell (that is, each individual PM and MM cell) into a 6x6 square of pixels, and records the fluorescence levels at each pixel in a file with extension .DAT. To summarize the fluorescence at each cell, MAS ignores the 20 border pixels and returns the 75th percentile fluorescence level of the remaining 16 pixels as the Average Intensity of the probe cell, and records these values in the .CEL file.
| | Sample_data_processing | Raw data reflecting hybridization intensities, from individual probes of 25 different chips were provided as Microarray Suite (MAS) 5.0 experiment data files: .CHP, .TXT, .RPT, .EXP, .CEL (the .TXT and .CEL files are linked below as supplementary files), and were normalised using d-Chip. Background information is provided on the website: http://biosun1.harvard.edu/complab/dchip/normalizing%20arrays.htm The normalized data were extracted into a Microsoft Excel file and hybridization intensities from all probes of the affected patients in individual families were compared to all of the other samples. Significance in multiplex families was tested using a one-tailed Student’s t-test assuming unequal variance, a Bonferroni correction and P-value < 0.05. In families with only one available patient, the transcript in that patient had to have a hybridization signal more than two standard deviations below the mean hybridization intensity in all other patients.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Dyonne,T.,Hartong
| | Sample_contact_email | d.t.hartong@ohk.umcg.nl
| | Sample_contact_laboratory | Ocular Molecular Genetics Institute
| | Sample_contact_department | Massachusetts Eye and Ear Infirmary
| | Sample_contact_institute | Harvard Medical School
| | Sample_contact_address | 243 Charles Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | MA 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305052/suppl/GSM305052.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305052/suppl/GSM305052.TXT.gz
| | Sample_series_id | GSE12086
| | Sample_data_row_count | 54613
| | |
|
GSM305053 | GPL570 |
|
lymphoblast_RPfamily_4_003-019
|
Lymphoblast cell line from transformed lymphocytes.
|
human_female_recessive retinitis pigmentosa_transformed lymphocyte
|
n/a
|
| Sample_geo_accession | GSM305053
| | Sample_status | Public on Jul 14 2008
| | Sample_submission_date | Jul 11 2008
| | Sample_last_update_date | Jul 14 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | none
| | Sample_growth_protocol_ch1 | Lymphoblasts were immortalized and grown at the Harvard Partners Center for Genetics and Genomics. Prior to harvesting for mRNA isolation, cells were grown to confluence in T25 flasks (10 ml media/flask), and then transferred to T75 flasks with an additional 15 ml of fresh media. When the cells reached confluence (typically after 3 - 6 weeks), another 25 ml of media was added, for a total of 50 ml. The cells were harvested 24 hours after adding media.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Harvested lymphoblast cell lines were pelleted by centrifugation at 1200 RPM at room temperature and washed twice with PBS buffer and repelleted. Cell pellet was suspended in 2 ml of Trizol, divided into 4 aliquots, and kept at -80 C. An aliquot of the lymphoblast-Trizol suspension was thawed and RNA was purified using the Promega SV Total RNA Isolation kit and resuspended in RNAse-free water.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was labeled at the Dana Farber Cancer Institute Microarray Core Facility using their standard protocol detailed below. 1. RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. 2. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. 3. The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. 4. The purified cRNA is fragmented in order to facilitate the subsequent hybridization step.
| | Sample_hyb_protocol | RNA was further processed at the Dana Farber Cancer Institute Microarray Core Facility using their standard protocol detailed below. 1. The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. 2. The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE. 3. Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.
| | Sample_scan_protocol | Affymetrix Microarray Suite 5.0 was used as scanning software. The target mRNA from the cell sample of interest is fragmented, fluorescently labeled, and washed over the array. Ideally, the components of the target mRNA sample will specifically hybridize to the intended PM strand. The MM strand serves as a control for non-specific cross-hybridization. The fluorescence levels at each PM and MM are then measured using a scanning microscope. MAS software outputs detected fluorescence levels at each probe. When the scanning microscope reads fluorescence activity, it dissects each probe cell (that is, each individual PM and MM cell) into a 6x6 square of pixels, and records the fluorescence levels at each pixel in a file with extension .DAT. To summarize the fluorescence at each cell, MAS ignores the 20 border pixels and returns the 75th percentile fluorescence level of the remaining 16 pixels as the Average Intensity of the probe cell, and records these values in the .CEL file.
| | Sample_data_processing | Raw data reflecting hybridization intensities, from individual probes of 25 different chips were provided as Microarray Suite (MAS) 5.0 experiment data files: .CHP, .TXT, .RPT, .EXP, .CEL (the .TXT and .CEL files are linked below as supplementary files), and were normalised using d-Chip. Background information is provided on the website: http://biosun1.harvard.edu/complab/dchip/normalizing%20arrays.htm The normalized data were extracted into a Microsoft Excel file and hybridization intensities from all probes of the affected patients in individual families were compared to all of the other samples. Significance in multiplex families was tested using a one-tailed Student’s t-test assuming unequal variance, a Bonferroni correction and P-value < 0.05. In families with only one available patient, the transcript in that patient had to have a hybridization signal more than two standard deviations below the mean hybridization intensity in all other patients.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Dyonne,T.,Hartong
| | Sample_contact_email | d.t.hartong@ohk.umcg.nl
| | Sample_contact_laboratory | Ocular Molecular Genetics Institute
| | Sample_contact_department | Massachusetts Eye and Ear Infirmary
| | Sample_contact_institute | Harvard Medical School
| | Sample_contact_address | 243 Charles Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | MA 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305053/suppl/GSM305053.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305053/suppl/GSM305053.TXT.gz
| | Sample_series_id | GSE12086
| | Sample_data_row_count | 54613
| | |
|
GSM305054 | GPL570 |
|
lymphoblast_RPfamily_4_218-340
|
Lymphoblast cell line from transformed lymphocytes.
|
human_male_recessive retinitis pigmentosa_transformed lymphocyte
|
n/a
|
| Sample_geo_accession | GSM305054
| | Sample_status | Public on Jul 14 2008
| | Sample_submission_date | Jul 11 2008
| | Sample_last_update_date | Jul 14 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | none
| | Sample_growth_protocol_ch1 | Lymphoblasts were immortalized and grown at the Harvard Partners Center for Genetics and Genomics. Prior to harvesting for mRNA isolation, cells were grown to confluence in T25 flasks (10 ml media/flask), and then transferred to T75 flasks with an additional 15 ml of fresh media. When the cells reached confluence (typically after 3 - 6 weeks), another 25 ml of media was added, for a total of 50 ml. The cells were harvested 24 hours after adding media.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Harvested lymphoblast cell lines were pelleted by centrifugation at 1200 RPM at room temperature and washed twice with PBS buffer and repelleted. Cell pellet was suspended in 2 ml of Trizol, divided into 4 aliquots, and kept at -80 C. An aliquot of the lymphoblast-Trizol suspension was thawed and RNA was purified using the Promega SV Total RNA Isolation kit and resuspended in RNAse-free water.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was labeled at the Dana Farber Cancer Institute Microarray Core Facility using their standard protocol detailed below. 1. RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. 2. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. 3. The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. 4. The purified cRNA is fragmented in order to facilitate the subsequent hybridization step.
| | Sample_hyb_protocol | RNA was further processed at the Dana Farber Cancer Institute Microarray Core Facility using their standard protocol detailed below. 1. The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. 2. The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE. 3. Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.
| | Sample_scan_protocol | Affymetrix Microarray Suite 5.0 was used as scanning software. The target mRNA from the cell sample of interest is fragmented, fluorescently labeled, and washed over the array. Ideally, the components of the target mRNA sample will specifically hybridize to the intended PM strand. The MM strand serves as a control for non-specific cross-hybridization. The fluorescence levels at each PM and MM are then measured using a scanning microscope. MAS software outputs detected fluorescence levels at each probe. When the scanning microscope reads fluorescence activity, it dissects each probe cell (that is, each individual PM and MM cell) into a 6x6 square of pixels, and records the fluorescence levels at each pixel in a file with extension .DAT. To summarize the fluorescence at each cell, MAS ignores the 20 border pixels and returns the 75th percentile fluorescence level of the remaining 16 pixels as the Average Intensity of the probe cell, and records these values in the .CEL file.
| | Sample_data_processing | Raw data reflecting hybridization intensities, from individual probes of 25 different chips were provided as Microarray Suite (MAS) 5.0 experiment data files: .CHP, .TXT, .RPT, .EXP, .CEL (the .TXT and .CEL files are linked below as supplementary files), and were normalised using d-Chip. Background information is provided on the website: http://biosun1.harvard.edu/complab/dchip/normalizing%20arrays.htm The normalized data were extracted into a Microsoft Excel file and hybridization intensities from all probes of the affected patients in individual families were compared to all of the other samples. Significance in multiplex families was tested using a one-tailed Student’s t-test assuming unequal variance, a Bonferroni correction and P-value < 0.05. In families with only one available patient, the transcript in that patient had to have a hybridization signal more than two standard deviations below the mean hybridization intensity in all other patients.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Dyonne,T.,Hartong
| | Sample_contact_email | d.t.hartong@ohk.umcg.nl
| | Sample_contact_laboratory | Ocular Molecular Genetics Institute
| | Sample_contact_department | Massachusetts Eye and Ear Infirmary
| | Sample_contact_institute | Harvard Medical School
| | Sample_contact_address | 243 Charles Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | MA 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305054/suppl/GSM305054.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305054/suppl/GSM305054.TXT.gz
| | Sample_series_id | GSE12086
| | Sample_data_row_count | 54613
| | |
|
GSM305055 | GPL570 |
|
lymphoblast_RPfamily_5_003-050
|
Lymphoblast cell line from transformed lymphocytes.
|
human_male_recessive retinitis pigmentosa_transformed lymphocyte
|
n/a
|
| Sample_geo_accession | GSM305055
| | Sample_status | Public on Jul 14 2008
| | Sample_submission_date | Jul 11 2008
| | Sample_last_update_date | Jul 14 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | none
| | Sample_growth_protocol_ch1 | Lymphoblasts were immortalized and grown at the Harvard Partners Center for Genetics and Genomics. Prior to harvesting for mRNA isolation, cells were grown to confluence in T25 flasks (10 ml media/flask), and then transferred to T75 flasks with an additional 15 ml of fresh media. When the cells reached confluence (typically after 3 - 6 weeks), another 25 ml of media was added, for a total of 50 ml. The cells were harvested 24 hours after adding media.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Harvested lymphoblast cell lines were pelleted by centrifugation at 1200 RPM at room temperature and washed twice with PBS buffer and repelleted. Cell pellet was suspended in 2 ml of Trizol, divided into 4 aliquots, and kept at -80 C. An aliquot of the lymphoblast-Trizol suspension was thawed and RNA was purified using the Promega SV Total RNA Isolation kit and resuspended in RNAse-free water.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was labeled at the Dana Farber Cancer Institute Microarray Core Facility using their standard protocol detailed below. 1. RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. 2. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. 3. The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. 4. The purified cRNA is fragmented in order to facilitate the subsequent hybridization step.
| | Sample_hyb_protocol | RNA was further processed at the Dana Farber Cancer Institute Microarray Core Facility using their standard protocol detailed below. 1. The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. 2. The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE. 3. Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.
| | Sample_scan_protocol | Affymetrix Microarray Suite 5.0 was used as scanning software. The target mRNA from the cell sample of interest is fragmented, fluorescently labeled, and washed over the array. Ideally, the components of the target mRNA sample will specifically hybridize to the intended PM strand. The MM strand serves as a control for non-specific cross-hybridization. The fluorescence levels at each PM and MM are then measured using a scanning microscope. MAS software outputs detected fluorescence levels at each probe. When the scanning microscope reads fluorescence activity, it dissects each probe cell (that is, each individual PM and MM cell) into a 6x6 square of pixels, and records the fluorescence levels at each pixel in a file with extension .DAT. To summarize the fluorescence at each cell, MAS ignores the 20 border pixels and returns the 75th percentile fluorescence level of the remaining 16 pixels as the Average Intensity of the probe cell, and records these values in the .CEL file.
| | Sample_data_processing | Raw data reflecting hybridization intensities, from individual probes of 25 different chips were provided as Microarray Suite (MAS) 5.0 experiment data files: .CHP, .TXT, .RPT, .EXP, .CEL (the .TXT and .CEL files are linked below as supplementary files), and were normalised using d-Chip. Background information is provided on the website: http://biosun1.harvard.edu/complab/dchip/normalizing%20arrays.htm The normalized data were extracted into a Microsoft Excel file and hybridization intensities from all probes of the affected patients in individual families were compared to all of the other samples. Significance in multiplex families was tested using a one-tailed Student’s t-test assuming unequal variance, a Bonferroni correction and P-value < 0.05. In families with only one available patient, the transcript in that patient had to have a hybridization signal more than two standard deviations below the mean hybridization intensity in all other patients.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Dyonne,T.,Hartong
| | Sample_contact_email | d.t.hartong@ohk.umcg.nl
| | Sample_contact_laboratory | Ocular Molecular Genetics Institute
| | Sample_contact_department | Massachusetts Eye and Ear Infirmary
| | Sample_contact_institute | Harvard Medical School
| | Sample_contact_address | 243 Charles Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | MA 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305055/suppl/GSM305055.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305055/suppl/GSM305055.TXT.gz
| | Sample_series_id | GSE12086
| | Sample_data_row_count | 54613
| | |
|
GSM305056 | GPL570 |
|
lymphoblast_RPfamily_5_226-065
|
Lymphoblast cell line from transformed lymphocytes.
|
human_female_recessive retinitis pigmentosa_transformed lymphocyte
|
n/a
|
| Sample_geo_accession | GSM305056
| | Sample_status | Public on Jul 14 2008
| | Sample_submission_date | Jul 11 2008
| | Sample_last_update_date | Jul 14 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | none
| | Sample_growth_protocol_ch1 | Lymphoblasts were immortalized and grown at the Harvard Partners Center for Genetics and Genomics. Prior to harvesting for mRNA isolation, cells were grown to confluence in T25 flasks (10 ml media/flask), and then transferred to T75 flasks with an additional 15 ml of fresh media. When the cells reached confluence (typically after 3 - 6 weeks), another 25 ml of media was added, for a total of 50 ml. The cells were harvested 24 hours after adding media.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Harvested lymphoblast cell lines were pelleted by centrifugation at 1200 RPM at room temperature and washed twice with PBS buffer and repelleted. Cell pellet was suspended in 2 ml of Trizol, divided into 4 aliquots, and kept at -80 C. An aliquot of the lymphoblast-Trizol suspension was thawed and RNA was purified using the Promega SV Total RNA Isolation kit and resuspended in RNAse-free water.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was labeled at the Dana Farber Cancer Institute Microarray Core Facility using their standard protocol detailed below. 1. RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. 2. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. 3. The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. 4. The purified cRNA is fragmented in order to facilitate the subsequent hybridization step.
| | Sample_hyb_protocol | RNA was further processed at the Dana Farber Cancer Institute Microarray Core Facility using their standard protocol detailed below. 1. The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. 2. The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE. 3. Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.
| | Sample_scan_protocol | Affymetrix Microarray Suite 5.0 was used as scanning software. The target mRNA from the cell sample of interest is fragmented, fluorescently labeled, and washed over the array. Ideally, the components of the target mRNA sample will specifically hybridize to the intended PM strand. The MM strand serves as a control for non-specific cross-hybridization. The fluorescence levels at each PM and MM are then measured using a scanning microscope. MAS software outputs detected fluorescence levels at each probe. When the scanning microscope reads fluorescence activity, it dissects each probe cell (that is, each individual PM and MM cell) into a 6x6 square of pixels, and records the fluorescence levels at each pixel in a file with extension .DAT. To summarize the fluorescence at each cell, MAS ignores the 20 border pixels and returns the 75th percentile fluorescence level of the remaining 16 pixels as the Average Intensity of the probe cell, and records these values in the .CEL file.
| | Sample_data_processing | Raw data reflecting hybridization intensities, from individual probes of 25 different chips were provided as Microarray Suite (MAS) 5.0 experiment data files: .CHP, .TXT, .RPT, .EXP, .CEL (the .TXT and .CEL files are linked below as supplementary files), and were normalised using d-Chip. Background information is provided on the website: http://biosun1.harvard.edu/complab/dchip/normalizing%20arrays.htm The normalized data were extracted into a Microsoft Excel file and hybridization intensities from all probes of the affected patients in individual families were compared to all of the other samples. Significance in multiplex families was tested using a one-tailed Student’s t-test assuming unequal variance, a Bonferroni correction and P-value < 0.05. In families with only one available patient, the transcript in that patient had to have a hybridization signal more than two standard deviations below the mean hybridization intensity in all other patients.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Dyonne,T.,Hartong
| | Sample_contact_email | d.t.hartong@ohk.umcg.nl
| | Sample_contact_laboratory | Ocular Molecular Genetics Institute
| | Sample_contact_department | Massachusetts Eye and Ear Infirmary
| | Sample_contact_institute | Harvard Medical School
| | Sample_contact_address | 243 Charles Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | MA 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305056/suppl/GSM305056.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305056/suppl/GSM305056.TXT.gz
| | Sample_series_id | GSE12086
| | Sample_data_row_count | 54613
| | |
|
GSM305057 | GPL570 |
|
lymphoblast_RPfamily_6_003-046
|
Lymphoblast cell line from transformed lymphocytes.
|
human_female_recessive retinitis pigmentosa_transformed lymphocyte
|
n/a
|
| Sample_geo_accession | GSM305057
| | Sample_status | Public on Jul 14 2008
| | Sample_submission_date | Jul 11 2008
| | Sample_last_update_date | Jul 14 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | none
| | Sample_growth_protocol_ch1 | Lymphoblasts were immortalized and grown at the Harvard Partners Center for Genetics and Genomics. Prior to harvesting for mRNA isolation, cells were grown to confluence in T25 flasks (10 ml media/flask), and then transferred to T75 flasks with an additional 15 ml of fresh media. When the cells reached confluence (typically after 3 - 6 weeks), another 25 ml of media was added, for a total of 50 ml. The cells were harvested 24 hours after adding media.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Harvested lymphoblast cell lines were pelleted by centrifugation at 1200 RPM at room temperature and washed twice with PBS buffer and repelleted. Cell pellet was suspended in 2 ml of Trizol, divided into 4 aliquots, and kept at -80 C. An aliquot of the lymphoblast-Trizol suspension was thawed and RNA was purified using the Promega SV Total RNA Isolation kit and resuspended in RNAse-free water.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was labeled at the Dana Farber Cancer Institute Microarray Core Facility using their standard protocol detailed below. 1. RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. 2. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. 3. The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. 4. The purified cRNA is fragmented in order to facilitate the subsequent hybridization step.
| | Sample_hyb_protocol | RNA was further processed at the Dana Farber Cancer Institute Microarray Core Facility using their standard protocol detailed below. 1. The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. 2. The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE. 3. Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.
| | Sample_scan_protocol | Affymetrix Microarray Suite 5.0 was used as scanning software. The target mRNA from the cell sample of interest is fragmented, fluorescently labeled, and washed over the array. Ideally, the components of the target mRNA sample will specifically hybridize to the intended PM strand. The MM strand serves as a control for non-specific cross-hybridization. The fluorescence levels at each PM and MM are then measured using a scanning microscope. MAS software outputs detected fluorescence levels at each probe. When the scanning microscope reads fluorescence activity, it dissects each probe cell (that is, each individual PM and MM cell) into a 6x6 square of pixels, and records the fluorescence levels at each pixel in a file with extension .DAT. To summarize the fluorescence at each cell, MAS ignores the 20 border pixels and returns the 75th percentile fluorescence level of the remaining 16 pixels as the Average Intensity of the probe cell, and records these values in the .CEL file.
| | Sample_data_processing | Raw data reflecting hybridization intensities, from individual probes of 25 different chips were provided as Microarray Suite (MAS) 5.0 experiment data files: .CHP, .TXT, .RPT, .EXP, .CEL (the .TXT and .CEL files are linked below as supplementary files), and were normalised using d-Chip. Background information is provided on the website: http://biosun1.harvard.edu/complab/dchip/normalizing%20arrays.htm The normalized data were extracted into a Microsoft Excel file and hybridization intensities from all probes of the affected patients in individual families were compared to all of the other samples. Significance in multiplex families was tested using a one-tailed Student’s t-test assuming unequal variance, a Bonferroni correction and P-value < 0.05. In families with only one available patient, the transcript in that patient had to have a hybridization signal more than two standard deviations below the mean hybridization intensity in all other patients.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Dyonne,T.,Hartong
| | Sample_contact_email | d.t.hartong@ohk.umcg.nl
| | Sample_contact_laboratory | Ocular Molecular Genetics Institute
| | Sample_contact_department | Massachusetts Eye and Ear Infirmary
| | Sample_contact_institute | Harvard Medical School
| | Sample_contact_address | 243 Charles Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | MA 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305057/suppl/GSM305057.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305057/suppl/GSM305057.TXT.gz
| | Sample_series_id | GSE12086
| | Sample_data_row_count | 54613
| | |
|
GSM305058 | GPL570 |
|
lymphoblast_RPfamily_6_219-002
|
Lymphoblast cell line from transformed lymphocytes.
|
human_female_recessive retinitis pigmentosa_transformed lymphocyte
|
n/a
|
| Sample_geo_accession | GSM305058
| | Sample_status | Public on Jul 14 2008
| | Sample_submission_date | Jul 11 2008
| | Sample_last_update_date | Jul 14 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | none
| | Sample_growth_protocol_ch1 | Lymphoblasts were immortalized and grown at the Harvard Partners Center for Genetics and Genomics. Prior to harvesting for mRNA isolation, cells were grown to confluence in T25 flasks (10 ml media/flask), and then transferred to T75 flasks with an additional 15 ml of fresh media. When the cells reached confluence (typically after 3 - 6 weeks), another 25 ml of media was added, for a total of 50 ml. The cells were harvested 24 hours after adding media.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Harvested lymphoblast cell lines were pelleted by centrifugation at 1200 RPM at room temperature and washed twice with PBS buffer and repelleted. Cell pellet was suspended in 2 ml of Trizol, divided into 4 aliquots, and kept at -80 C. An aliquot of the lymphoblast-Trizol suspension was thawed and RNA was purified using the Promega SV Total RNA Isolation kit and resuspended in RNAse-free water.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was labeled at the Dana Farber Cancer Institute Microarray Core Facility using their standard protocol detailed below. 1. RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. 2. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. 3. The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. 4. The purified cRNA is fragmented in order to facilitate the subsequent hybridization step.
| | Sample_hyb_protocol | RNA was further processed at the Dana Farber Cancer Institute Microarray Core Facility using their standard protocol detailed below. 1. The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. 2. The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE. 3. Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.
| | Sample_scan_protocol | Affymetrix Microarray Suite 5.0 was used as scanning software. The target mRNA from the cell sample of interest is fragmented, fluorescently labeled, and washed over the array. Ideally, the components of the target mRNA sample will specifically hybridize to the intended PM strand. The MM strand serves as a control for non-specific cross-hybridization. The fluorescence levels at each PM and MM are then measured using a scanning microscope. MAS software outputs detected fluorescence levels at each probe. When the scanning microscope reads fluorescence activity, it dissects each probe cell (that is, each individual PM and MM cell) into a 6x6 square of pixels, and records the fluorescence levels at each pixel in a file with extension .DAT. To summarize the fluorescence at each cell, MAS ignores the 20 border pixels and returns the 75th percentile fluorescence level of the remaining 16 pixels as the Average Intensity of the probe cell, and records these values in the .CEL file.
| | Sample_data_processing | Raw data reflecting hybridization intensities, from individual probes of 25 different chips were provided as Microarray Suite (MAS) 5.0 experiment data files: .CHP, .TXT, .RPT, .EXP, .CEL (the .TXT and .CEL files are linked below as supplementary files), and were normalised using d-Chip. Background information is provided on the website: http://biosun1.harvard.edu/complab/dchip/normalizing%20arrays.htm The normalized data were extracted into a Microsoft Excel file and hybridization intensities from all probes of the affected patients in individual families were compared to all of the other samples. Significance in multiplex families was tested using a one-tailed Student’s t-test assuming unequal variance, a Bonferroni correction and P-value < 0.05. In families with only one available patient, the transcript in that patient had to have a hybridization signal more than two standard deviations below the mean hybridization intensity in all other patients.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Dyonne,T.,Hartong
| | Sample_contact_email | d.t.hartong@ohk.umcg.nl
| | Sample_contact_laboratory | Ocular Molecular Genetics Institute
| | Sample_contact_department | Massachusetts Eye and Ear Infirmary
| | Sample_contact_institute | Harvard Medical School
| | Sample_contact_address | 243 Charles Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | MA 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305058/suppl/GSM305058.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305058/suppl/GSM305058.TXT.gz
| | Sample_series_id | GSE12086
| | Sample_data_row_count | 54613
| | |
|
GSM305059 | GPL570 |
|
lymphoblast_RPfamily_6_219-004
|
Lymphoblast cell line from transformed lymphocytes.
|
human_male_recessive retinitis pigmentosa_transformed lymphocyte
|
n/a
|
| Sample_geo_accession | GSM305059
| | Sample_status | Public on Jul 14 2008
| | Sample_submission_date | Jul 11 2008
| | Sample_last_update_date | Jul 14 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | none
| | Sample_growth_protocol_ch1 | Lymphoblasts were immortalized and grown at the Harvard Partners Center for Genetics and Genomics. Prior to harvesting for mRNA isolation, cells were grown to confluence in T25 flasks (10 ml media/flask), and then transferred to T75 flasks with an additional 15 ml of fresh media. When the cells reached confluence (typically after 3 - 6 weeks), another 25 ml of media was added, for a total of 50 ml. The cells were harvested 24 hours after adding media.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Harvested lymphoblast cell lines were pelleted by centrifugation at 1200 RPM at room temperature and washed twice with PBS buffer and repelleted. Cell pellet was suspended in 2 ml of Trizol, divided into 4 aliquots, and kept at -80 C. An aliquot of the lymphoblast-Trizol suspension was thawed and RNA was purified using the Promega SV Total RNA Isolation kit and resuspended in RNAse-free water.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was labeled at the Dana Farber Cancer Institute Microarray Core Facility using their standard protocol detailed below. 1. RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. 2. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. 3. The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. 4. The purified cRNA is fragmented in order to facilitate the subsequent hybridization step.
| | Sample_hyb_protocol | RNA was further processed at the Dana Farber Cancer Institute Microarray Core Facility using their standard protocol detailed below. 1. The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. 2. The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE. 3. Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.
| | Sample_scan_protocol | Affymetrix Microarray Suite 5.0 was used as scanning software. The target mRNA from the cell sample of interest is fragmented, fluorescently labeled, and washed over the array. Ideally, the components of the target mRNA sample will specifically hybridize to the intended PM strand. The MM strand serves as a control for non-specific cross-hybridization. The fluorescence levels at each PM and MM are then measured using a scanning microscope. MAS software outputs detected fluorescence levels at each probe. When the scanning microscope reads fluorescence activity, it dissects each probe cell (that is, each individual PM and MM cell) into a 6x6 square of pixels, and records the fluorescence levels at each pixel in a file with extension .DAT. To summarize the fluorescence at each cell, MAS ignores the 20 border pixels and returns the 75th percentile fluorescence level of the remaining 16 pixels as the Average Intensity of the probe cell, and records these values in the .CEL file.
| | Sample_data_processing | Raw data reflecting hybridization intensities, from individual probes of 25 different chips were provided as Microarray Suite (MAS) 5.0 experiment data files: .CHP, .TXT, .RPT, .EXP, .CEL (the .TXT and .CEL files are linked below as supplementary files), and were normalised using d-Chip. Background information is provided on the website: http://biosun1.harvard.edu/complab/dchip/normalizing%20arrays.htm The normalized data were extracted into a Microsoft Excel file and hybridization intensities from all probes of the affected patients in individual families were compared to all of the other samples. Significance in multiplex families was tested using a one-tailed Student’s t-test assuming unequal variance, a Bonferroni correction and P-value < 0.05. In families with only one available patient, the transcript in that patient had to have a hybridization signal more than two standard deviations below the mean hybridization intensity in all other patients.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Dyonne,T.,Hartong
| | Sample_contact_email | d.t.hartong@ohk.umcg.nl
| | Sample_contact_laboratory | Ocular Molecular Genetics Institute
| | Sample_contact_department | Massachusetts Eye and Ear Infirmary
| | Sample_contact_institute | Harvard Medical School
| | Sample_contact_address | 243 Charles Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | MA 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305059/suppl/GSM305059.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305059/suppl/GSM305059.TXT.gz
| | Sample_series_id | GSE12086
| | Sample_data_row_count | 54613
| | |
|
GSM305060 | GPL570 |
|
lymphoblast_RPfamily_6_219-003
|
Lymphoblast cell line from transformed lymphocytes.
|
human_male_recessive retinitis pigmentosa_transformed lymphocyte
|
n/a
|
| Sample_geo_accession | GSM305060
| | Sample_status | Public on Jul 14 2008
| | Sample_submission_date | Jul 11 2008
| | Sample_last_update_date | Jul 14 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | none
| | Sample_growth_protocol_ch1 | Lymphoblasts were immortalized and grown at the Harvard Partners Center for Genetics and Genomics. Prior to harvesting for mRNA isolation, cells were grown to confluence in T25 flasks (10 ml media/flask), and then transferred to T75 flasks with an additional 15 ml of fresh media. When the cells reached confluence (typically after 3 - 6 weeks), another 25 ml of media was added, for a total of 50 ml. The cells were harvested 24 hours after adding media.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Harvested lymphoblast cell lines were pelleted by centrifugation at 1200 RPM at room temperature and washed twice with PBS buffer and repelleted. Cell pellet was suspended in 2 ml of Trizol, divided into 4 aliquots, and kept at -80 C. An aliquot of the lymphoblast-Trizol suspension was thawed and RNA was purified using the Promega SV Total RNA Isolation kit and resuspended in RNAse-free water.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was labeled at the Dana Farber Cancer Institute Microarray Core Facility using their standard protocol detailed below. 1. RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. 2. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. 3. The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. 4. The purified cRNA is fragmented in order to facilitate the subsequent hybridization step.
| | Sample_hyb_protocol | RNA was further processed at the Dana Farber Cancer Institute Microarray Core Facility using their standard protocol detailed below. 1. The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. 2. The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE. 3. Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.
| | Sample_scan_protocol | Affymetrix Microarray Suite 5.0 was used as scanning software. The target mRNA from the cell sample of interest is fragmented, fluorescently labeled, and washed over the array. Ideally, the components of the target mRNA sample will specifically hybridize to the intended PM strand. The MM strand serves as a control for non-specific cross-hybridization. The fluorescence levels at each PM and MM are then measured using a scanning microscope. MAS software outputs detected fluorescence levels at each probe. When the scanning microscope reads fluorescence activity, it dissects each probe cell (that is, each individual PM and MM cell) into a 6x6 square of pixels, and records the fluorescence levels at each pixel in a file with extension .DAT. To summarize the fluorescence at each cell, MAS ignores the 20 border pixels and returns the 75th percentile fluorescence level of the remaining 16 pixels as the Average Intensity of the probe cell, and records these values in the .CEL file.
| | Sample_data_processing | Raw data reflecting hybridization intensities, from individual probes of 25 different chips were provided as Microarray Suite (MAS) 5.0 experiment data files: .CHP, .TXT, .RPT, .EXP, .CEL (the .TXT and .CEL files are linked below as supplementary files), and were normalised using d-Chip. Background information is provided on the website: http://biosun1.harvard.edu/complab/dchip/normalizing%20arrays.htm The normalized data were extracted into a Microsoft Excel file and hybridization intensities from all probes of the affected patients in individual families were compared to all of the other samples. Significance in multiplex families was tested using a one-tailed Student’s t-test assuming unequal variance, a Bonferroni correction and P-value < 0.05. In families with only one available patient, the transcript in that patient had to have a hybridization signal more than two standard deviations below the mean hybridization intensity in all other patients.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Dyonne,T.,Hartong
| | Sample_contact_email | d.t.hartong@ohk.umcg.nl
| | Sample_contact_laboratory | Ocular Molecular Genetics Institute
| | Sample_contact_department | Massachusetts Eye and Ear Infirmary
| | Sample_contact_institute | Harvard Medical School
| | Sample_contact_address | 243 Charles Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | MA 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305060/suppl/GSM305060.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305060/suppl/GSM305060.TXT.gz
| | Sample_series_id | GSE12086
| | Sample_data_row_count | 54613
| | |
|
GSM305061 | GPL570 |
|
lymphoblast_RPisolate_003-053
|
Lymphoblast cell line from transformed lymphocytes.
|
human_female_recessive retinitis pigmentosa_transformed lymphocyte
|
n/a
|
| Sample_geo_accession | GSM305061
| | Sample_status | Public on Jul 14 2008
| | Sample_submission_date | Jul 11 2008
| | Sample_last_update_date | Jul 14 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | none
| | Sample_growth_protocol_ch1 | Lymphoblasts were immortalized and grown at the Harvard Partners Center for Genetics and Genomics. Prior to harvesting for mRNA isolation, cells were grown to confluence in T25 flasks (10 ml media/flask), and then transferred to T75 flasks with an additional 15 ml of fresh media. When the cells reached confluence (typically after 3 - 6 weeks), another 25 ml of media was added, for a total of 50 ml. The cells were harvested 24 hours after adding media.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Harvested lymphoblast cell lines were pelleted by centrifugation at 1200 RPM at room temperature and washed twice with PBS buffer and repelleted. Cell pellet was suspended in 2 ml of Trizol, divided into 4 aliquots, and kept at -80 C. An aliquot of the lymphoblast-Trizol suspension was thawed and RNA was purified using the Promega SV Total RNA Isolation kit and resuspended in RNAse-free water.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was labeled at the Dana Farber Cancer Institute Microarray Core Facility using their standard protocol detailed below. 1. RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. 2. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. 3. The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. 4. The purified cRNA is fragmented in order to facilitate the subsequent hybridization step.
| | Sample_hyb_protocol | RNA was further processed at the Dana Farber Cancer Institute Microarray Core Facility using their standard protocol detailed below. 1. The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. 2. The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE. 3. Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.
| | Sample_scan_protocol | Affymetrix Microarray Suite 5.0 was used as scanning software. The target mRNA from the cell sample of interest is fragmented, fluorescently labeled, and washed over the array. Ideally, the components of the target mRNA sample will specifically hybridize to the intended PM strand. The MM strand serves as a control for non-specific cross-hybridization. The fluorescence levels at each PM and MM are then measured using a scanning microscope. MAS software outputs detected fluorescence levels at each probe. When the scanning microscope reads fluorescence activity, it dissects each probe cell (that is, each individual PM and MM cell) into a 6x6 square of pixels, and records the fluorescence levels at each pixel in a file with extension .DAT. To summarize the fluorescence at each cell, MAS ignores the 20 border pixels and returns the 75th percentile fluorescence level of the remaining 16 pixels as the Average Intensity of the probe cell, and records these values in the .CEL file.
| | Sample_data_processing | Raw data reflecting hybridization intensities, from individual probes of 25 different chips were provided as Microarray Suite (MAS) 5.0 experiment data files: .CHP, .TXT, .RPT, .EXP, .CEL (the .TXT and .CEL files are linked below as supplementary files), and were normalised using d-Chip. Background information is provided on the website: http://biosun1.harvard.edu/complab/dchip/normalizing%20arrays.htm The normalized data were extracted into a Microsoft Excel file and hybridization intensities from all probes of the affected patients in individual families were compared to all of the other samples. Significance in multiplex families was tested using a one-tailed Student’s t-test assuming unequal variance, a Bonferroni correction and P-value < 0.05. In families with only one available patient, the transcript in that patient had to have a hybridization signal more than two standard deviations below the mean hybridization intensity in all other patients.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Dyonne,T.,Hartong
| | Sample_contact_email | d.t.hartong@ohk.umcg.nl
| | Sample_contact_laboratory | Ocular Molecular Genetics Institute
| | Sample_contact_department | Massachusetts Eye and Ear Infirmary
| | Sample_contact_institute | Harvard Medical School
| | Sample_contact_address | 243 Charles Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | MA 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305061/suppl/GSM305061.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305061/suppl/GSM305061.TXT.gz
| | Sample_series_id | GSE12086
| | Sample_data_row_count | 54613
| | |
|
GSM305062 | GPL570 |
|
lymphoblast_RPisolate_003-146
|
Lymphoblast cell line from transformed lymphocytes.
|
human_male_recessive retinitis pigmentosa_transformed lymphocyte
|
n/a
|
| Sample_geo_accession | GSM305062
| | Sample_status | Public on Jul 14 2008
| | Sample_submission_date | Jul 11 2008
| | Sample_last_update_date | Jul 14 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | none
| | Sample_growth_protocol_ch1 | Lymphoblasts were immortalized and grown at the Harvard Partners Center for Genetics and Genomics. Prior to harvesting for mRNA isolation, cells were grown to confluence in T25 flasks (10 ml media/flask), and then transferred to T75 flasks with an additional 15 ml of fresh media. When the cells reached confluence (typically after 3 - 6 weeks), another 25 ml of media was added, for a total of 50 ml. The cells were harvested 24 hours after adding media.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Harvested lymphoblast cell lines were pelleted by centrifugation at 1200 RPM at room temperature and washed twice with PBS buffer and repelleted. Cell pellet was suspended in 2 ml of Trizol, divided into 4 aliquots, and kept at -80 C. An aliquot of the lymphoblast-Trizol suspension was thawed and RNA was purified using the Promega SV Total RNA Isolation kit and resuspended in RNAse-free water.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was labeled at the Dana Farber Cancer Institute Microarray Core Facility using their standard protocol detailed below. 1. RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. 2. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. 3. The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. 4. The purified cRNA is fragmented in order to facilitate the subsequent hybridization step.
| | Sample_hyb_protocol | RNA was further processed at the Dana Farber Cancer Institute Microarray Core Facility using their standard protocol detailed below. 1. The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. 2. The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE. 3. Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.
| | Sample_scan_protocol | Affymetrix Microarray Suite 5.0 was used as scanning software. The target mRNA from the cell sample of interest is fragmented, fluorescently labeled, and washed over the array. Ideally, the components of the target mRNA sample will specifically hybridize to the intended PM strand. The MM strand serves as a control for non-specific cross-hybridization. The fluorescence levels at each PM and MM are then measured using a scanning microscope. MAS software outputs detected fluorescence levels at each probe. When the scanning microscope reads fluorescence activity, it dissects each probe cell (that is, each individual PM and MM cell) into a 6x6 square of pixels, and records the fluorescence levels at each pixel in a file with extension .DAT. To summarize the fluorescence at each cell, MAS ignores the 20 border pixels and returns the 75th percentile fluorescence level of the remaining 16 pixels as the Average Intensity of the probe cell, and records these values in the .CEL file.
| | Sample_data_processing | Raw data reflecting hybridization intensities, from individual probes of 25 different chips were provided as Microarray Suite (MAS) 5.0 experiment data files: .CHP, .TXT, .RPT, .EXP, .CEL (the .TXT and .CEL files are linked below as supplementary files), and were normalised using d-Chip. Background information is provided on the website: http://biosun1.harvard.edu/complab/dchip/normalizing%20arrays.htm The normalized data were extracted into a Microsoft Excel file and hybridization intensities from all probes of the affected patients in individual families were compared to all of the other samples. Significance in multiplex families was tested using a one-tailed Student’s t-test assuming unequal variance, a Bonferroni correction and P-value < 0.05. In families with only one available patient, the transcript in that patient had to have a hybridization signal more than two standard deviations below the mean hybridization intensity in all other patients.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Dyonne,T.,Hartong
| | Sample_contact_email | d.t.hartong@ohk.umcg.nl
| | Sample_contact_laboratory | Ocular Molecular Genetics Institute
| | Sample_contact_department | Massachusetts Eye and Ear Infirmary
| | Sample_contact_institute | Harvard Medical School
| | Sample_contact_address | 243 Charles Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | MA 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305062/suppl/GSM305062.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305062/suppl/GSM305062.TXT.gz
| | Sample_series_id | GSE12086
| | Sample_data_row_count | 54613
| | |
|
GSM305063 | GPL570 |
|
lymphoblast_RPisolate_003-115
|
Lymphoblast cell line from transformed lymphocytes.
|
human_female_recessive retinitis pigmentosa_transformed lymphocyte
|
n/a
|
| Sample_geo_accession | GSM305063
| | Sample_status | Public on Jul 14 2008
| | Sample_submission_date | Jul 11 2008
| | Sample_last_update_date | Jul 14 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | none
| | Sample_growth_protocol_ch1 | Lymphoblasts were immortalized and grown at the Harvard Partners Center for Genetics and Genomics. Prior to harvesting for mRNA isolation, cells were grown to confluence in T25 flasks (10 ml media/flask), and then transferred to T75 flasks with an additional 15 ml of fresh media. When the cells reached confluence (typically after 3 - 6 weeks), another 25 ml of media was added, for a total of 50 ml. The cells were harvested 24 hours after adding media.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Harvested lymphoblast cell lines were pelleted by centrifugation at 1200 RPM at room temperature and washed twice with PBS buffer and repelleted. Cell pellet was suspended in 2 ml of Trizol, divided into 4 aliquots, and kept at -80 C. An aliquot of the lymphoblast-Trizol suspension was thawed and RNA was purified using the Promega SV Total RNA Isolation kit and resuspended in RNAse-free water.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was labeled at the Dana Farber Cancer Institute Microarray Core Facility using their standard protocol detailed below. 1. RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. 2. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. 3. The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. 4. The purified cRNA is fragmented in order to facilitate the subsequent hybridization step.
| | Sample_hyb_protocol | RNA was further processed at the Dana Farber Cancer Institute Microarray Core Facility using their standard protocol detailed below. 1. The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. 2. The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE. 3. Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.
| | Sample_scan_protocol | Affymetrix Microarray Suite 5.0 was used as scanning software. The target mRNA from the cell sample of interest is fragmented, fluorescently labeled, and washed over the array. Ideally, the components of the target mRNA sample will specifically hybridize to the intended PM strand. The MM strand serves as a control for non-specific cross-hybridization. The fluorescence levels at each PM and MM are then measured using a scanning microscope. MAS software outputs detected fluorescence levels at each probe. When the scanning microscope reads fluorescence activity, it dissects each probe cell (that is, each individual PM and MM cell) into a 6x6 square of pixels, and records the fluorescence levels at each pixel in a file with extension .DAT. To summarize the fluorescence at each cell, MAS ignores the 20 border pixels and returns the 75th percentile fluorescence level of the remaining 16 pixels as the Average Intensity of the probe cell, and records these values in the .CEL file.
| | Sample_data_processing | Raw data reflecting hybridization intensities, from individual probes of 25 different chips were provided as Microarray Suite (MAS) 5.0 experiment data files: .CHP, .TXT, .RPT, .EXP, .CEL (the .TXT and .CEL files are linked below as supplementary files), and were normalised using d-Chip. Background information is provided on the website: http://biosun1.harvard.edu/complab/dchip/normalizing%20arrays.htm The normalized data were extracted into a Microsoft Excel file and hybridization intensities from all probes of the affected patients in individual families were compared to all of the other samples. Significance in multiplex families was tested using a one-tailed Student’s t-test assuming unequal variance, a Bonferroni correction and P-value < 0.05. In families with only one available patient, the transcript in that patient had to have a hybridization signal more than two standard deviations below the mean hybridization intensity in all other patients.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Dyonne,T.,Hartong
| | Sample_contact_email | d.t.hartong@ohk.umcg.nl
| | Sample_contact_laboratory | Ocular Molecular Genetics Institute
| | Sample_contact_department | Massachusetts Eye and Ear Infirmary
| | Sample_contact_institute | Harvard Medical School
| | Sample_contact_address | 243 Charles Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | MA 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305063/suppl/GSM305063.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305063/suppl/GSM305063.TXT.gz
| | Sample_series_id | GSE12086
| | Sample_data_row_count | 54613
| | |
|
GSM305064 | GPL570 |
|
lymphoblast_RPisolate_003-131
|
Lymphoblast cell line from transformed lymphocytes.
|
human_female_recessive retinitis pigmentosa_transformed lymphocyte
|
n/a
|
| Sample_geo_accession | GSM305064
| | Sample_status | Public on Jul 14 2008
| | Sample_submission_date | Jul 11 2008
| | Sample_last_update_date | Jul 14 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | none
| | Sample_growth_protocol_ch1 | Lymphoblasts were immortalized and grown at the Harvard Partners Center for Genetics and Genomics. Prior to harvesting for mRNA isolation, cells were grown to confluence in T25 flasks (10 ml media/flask), and then transferred to T75 flasks with an additional 15 ml of fresh media. When the cells reached confluence (typically after 3 - 6 weeks), another 25 ml of media was added, for a total of 50 ml. The cells were harvested 24 hours after adding media.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Harvested lymphoblast cell lines were pelleted by centrifugation at 1200 RPM at room temperature and washed twice with PBS buffer and repelleted. Cell pellet was suspended in 2 ml of Trizol, divided into 4 aliquots, and kept at -80 C. An aliquot of the lymphoblast-Trizol suspension was thawed and RNA was purified using the Promega SV Total RNA Isolation kit and resuspended in RNAse-free water.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was labeled at the Dana Farber Cancer Institute Microarray Core Facility using their standard protocol detailed below. 1. RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. 2. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. 3. The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. 4. The purified cRNA is fragmented in order to facilitate the subsequent hybridization step.
| | Sample_hyb_protocol | RNA was further processed at the Dana Farber Cancer Institute Microarray Core Facility using their standard protocol detailed below. 1. The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. 2. The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE. 3. Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.
| | Sample_scan_protocol | Affymetrix Microarray Suite 5.0 was used as scanning software. The target mRNA from the cell sample of interest is fragmented, fluorescently labeled, and washed over the array. Ideally, the components of the target mRNA sample will specifically hybridize to the intended PM strand. The MM strand serves as a control for non-specific cross-hybridization. The fluorescence levels at each PM and MM are then measured using a scanning microscope. MAS software outputs detected fluorescence levels at each probe. When the scanning microscope reads fluorescence activity, it dissects each probe cell (that is, each individual PM and MM cell) into a 6x6 square of pixels, and records the fluorescence levels at each pixel in a file with extension .DAT. To summarize the fluorescence at each cell, MAS ignores the 20 border pixels and returns the 75th percentile fluorescence level of the remaining 16 pixels as the Average Intensity of the probe cell, and records these values in the .CEL file.
| | Sample_data_processing | Raw data reflecting hybridization intensities, from individual probes of 25 different chips were provided as Microarray Suite (MAS) 5.0 experiment data files: .CHP, .TXT, .RPT, .EXP, .CEL (the .TXT and .CEL files are linked below as supplementary files), and were normalised using d-Chip. Background information is provided on the website: http://biosun1.harvard.edu/complab/dchip/normalizing%20arrays.htm The normalized data were extracted into a Microsoft Excel file and hybridization intensities from all probes of the affected patients in individual families were compared to all of the other samples. Significance in multiplex families was tested using a one-tailed Student’s t-test assuming unequal variance, a Bonferroni correction and P-value < 0.05. In families with only one available patient, the transcript in that patient had to have a hybridization signal more than two standard deviations below the mean hybridization intensity in all other patients.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Dyonne,T.,Hartong
| | Sample_contact_email | d.t.hartong@ohk.umcg.nl
| | Sample_contact_laboratory | Ocular Molecular Genetics Institute
| | Sample_contact_department | Massachusetts Eye and Ear Infirmary
| | Sample_contact_institute | Harvard Medical School
| | Sample_contact_address | 243 Charles Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | MA 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305064/suppl/GSM305064.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305064/suppl/GSM305064.TXT.gz
| | Sample_series_id | GSE12086
| | Sample_data_row_count | 54613
| | |
|
GSM305065 | GPL570 |
|
lymphoblast_RPisolate_003-173
|
Lymphoblast cell line from transformed lymphocytes.
|
human_male_recessive retinitis pigmentosa_transformed lymphocyte
|
n/a
|
| Sample_geo_accession | GSM305065
| | Sample_status | Public on Jul 14 2008
| | Sample_submission_date | Jul 11 2008
| | Sample_last_update_date | Jul 14 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | none
| | Sample_growth_protocol_ch1 | Lymphoblasts were immortalized and grown at the Harvard Partners Center for Genetics and Genomics. Prior to harvesting for mRNA isolation, cells were grown to confluence in T25 flasks (10 ml media/flask), and then transferred to T75 flasks with an additional 15 ml of fresh media. When the cells reached confluence (typically after 3 - 6 weeks), another 25 ml of media was added, for a total of 50 ml. The cells were harvested 24 hours after adding media.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Harvested lymphoblast cell lines were pelleted by centrifugation at 1200 RPM at room temperature and washed twice with PBS buffer and repelleted. Cell pellet was suspended in 2 ml of Trizol, divided into 4 aliquots, and kept at -80 C. An aliquot of the lymphoblast-Trizol suspension was thawed and RNA was purified using the Promega SV Total RNA Isolation kit and resuspended in RNAse-free water.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was labeled at the Dana Farber Cancer Institute Microarray Core Facility using their standard protocol detailed below. 1. RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. 2. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. 3. The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. 4. The purified cRNA is fragmented in order to facilitate the subsequent hybridization step.
| | Sample_hyb_protocol | RNA was further processed at the Dana Farber Cancer Institute Microarray Core Facility using their standard protocol detailed below. 1. The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. 2. The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE. 3. Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.
| | Sample_scan_protocol | Affymetrix Microarray Suite 5.0 was used as scanning software. The target mRNA from the cell sample of interest is fragmented, fluorescently labeled, and washed over the array. Ideally, the components of the target mRNA sample will specifically hybridize to the intended PM strand. The MM strand serves as a control for non-specific cross-hybridization. The fluorescence levels at each PM and MM are then measured using a scanning microscope. MAS software outputs detected fluorescence levels at each probe. When the scanning microscope reads fluorescence activity, it dissects each probe cell (that is, each individual PM and MM cell) into a 6x6 square of pixels, and records the fluorescence levels at each pixel in a file with extension .DAT. To summarize the fluorescence at each cell, MAS ignores the 20 border pixels and returns the 75th percentile fluorescence level of the remaining 16 pixels as the Average Intensity of the probe cell, and records these values in the .CEL file.
| | Sample_data_processing | Raw data reflecting hybridization intensities, from individual probes of 25 different chips were provided as Microarray Suite (MAS) 5.0 experiment data files: .CHP, .TXT, .RPT, .EXP, .CEL (the .TXT and .CEL files are linked below as supplementary files), and were normalised using d-Chip. Background information is provided on the website: http://biosun1.harvard.edu/complab/dchip/normalizing%20arrays.htm The normalized data were extracted into a Microsoft Excel file and hybridization intensities from all probes of the affected patients in individual families were compared to all of the other samples. Significance in multiplex families was tested using a one-tailed Student’s t-test assuming unequal variance, a Bonferroni correction and P-value < 0.05. In families with only one available patient, the transcript in that patient had to have a hybridization signal more than two standard deviations below the mean hybridization intensity in all other patients.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Dyonne,T.,Hartong
| | Sample_contact_email | d.t.hartong@ohk.umcg.nl
| | Sample_contact_laboratory | Ocular Molecular Genetics Institute
| | Sample_contact_department | Massachusetts Eye and Ear Infirmary
| | Sample_contact_institute | Harvard Medical School
| | Sample_contact_address | 243 Charles Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | MA 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305065/suppl/GSM305065.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305065/suppl/GSM305065.TXT.gz
| | Sample_series_id | GSE12086
| | Sample_data_row_count | 54613
| | |
|
GSM305066 | GPL570 |
|
lymphoblast_RPisolate_003-162
|
Lymphoblast cell line from transformed lymphocytes.
|
human_male_recessive retinitis pigmentosa_transformed lymphocyte
|
n/a
|
| Sample_geo_accession | GSM305066
| | Sample_status | Public on Jul 14 2008
| | Sample_submission_date | Jul 11 2008
| | Sample_last_update_date | Jul 14 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | none
| | Sample_growth_protocol_ch1 | Lymphoblasts were immortalized and grown at the Harvard Partners Center for Genetics and Genomics. Prior to harvesting for mRNA isolation, cells were grown to confluence in T25 flasks (10 ml media/flask), and then transferred to T75 flasks with an additional 15 ml of fresh media. When the cells reached confluence (typically after 3 - 6 weeks), another 25 ml of media was added, for a total of 50 ml. The cells were harvested 24 hours after adding media.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Harvested lymphoblast cell lines were pelleted by centrifugation at 1200 RPM at room temperature and washed twice with PBS buffer and repelleted. Cell pellet was suspended in 2 ml of Trizol, divided into 4 aliquots, and kept at -80 C. An aliquot of the lymphoblast-Trizol suspension was thawed and RNA was purified using the Promega SV Total RNA Isolation kit and resuspended in RNAse-free water.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was labeled at the Dana Farber Cancer Institute Microarray Core Facility using their standard protocol detailed below. 1. RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. 2. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. 3. The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. 4. The purified cRNA is fragmented in order to facilitate the subsequent hybridization step.
| | Sample_hyb_protocol | RNA was further processed at the Dana Farber Cancer Institute Microarray Core Facility using their standard protocol detailed below. 1. The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. 2. The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE. 3. Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.
| | Sample_scan_protocol | Affymetrix Microarray Suite 5.0 was used as scanning software. The target mRNA from the cell sample of interest is fragmented, fluorescently labeled, and washed over the array. Ideally, the components of the target mRNA sample will specifically hybridize to the intended PM strand. The MM strand serves as a control for non-specific cross-hybridization. The fluorescence levels at each PM and MM are then measured using a scanning microscope. MAS software outputs detected fluorescence levels at each probe. When the scanning microscope reads fluorescence activity, it dissects each probe cell (that is, each individual PM and MM cell) into a 6x6 square of pixels, and records the fluorescence levels at each pixel in a file with extension .DAT. To summarize the fluorescence at each cell, MAS ignores the 20 border pixels and returns the 75th percentile fluorescence level of the remaining 16 pixels as the Average Intensity of the probe cell, and records these values in the .CEL file.
| | Sample_data_processing | Raw data reflecting hybridization intensities, from individual probes of 25 different chips were provided as Microarray Suite (MAS) 5.0 experiment data files: .CHP, .TXT, .RPT, .EXP, .CEL (the .TXT and .CEL files are linked below as supplementary files), and were normalised using d-Chip. Background information is provided on the website: http://biosun1.harvard.edu/complab/dchip/normalizing%20arrays.htm The normalized data were extracted into a Microsoft Excel file and hybridization intensities from all probes of the affected patients in individual families were compared to all of the other samples. Significance in multiplex families was tested using a one-tailed Student’s t-test assuming unequal variance, a Bonferroni correction and P-value < 0.05. In families with only one available patient, the transcript in that patient had to have a hybridization signal more than two standard deviations below the mean hybridization intensity in all other patients.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Dyonne,T.,Hartong
| | Sample_contact_email | d.t.hartong@ohk.umcg.nl
| | Sample_contact_laboratory | Ocular Molecular Genetics Institute
| | Sample_contact_department | Massachusetts Eye and Ear Infirmary
| | Sample_contact_institute | Harvard Medical School
| | Sample_contact_address | 243 Charles Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | MA 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305066/suppl/GSM305066.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305066/suppl/GSM305066.TXT.gz
| | Sample_series_id | GSE12086
| | Sample_data_row_count | 54613
| | |
|
GSM305067 | GPL570 |
|
lymphoblast_RPisolate_003-152
|
Lymphoblast cell line from transformed lymphocytes.
|
human_female_recessive retinitis pigmentosa_transformed lymphocyte
|
n/a
|
| Sample_geo_accession | GSM305067
| | Sample_status | Public on Jul 14 2008
| | Sample_submission_date | Jul 11 2008
| | Sample_last_update_date | Jul 14 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | none
| | Sample_growth_protocol_ch1 | Lymphoblasts were immortalized and grown at the Harvard Partners Center for Genetics and Genomics. Prior to harvesting for mRNA isolation, cells were grown to confluence in T25 flasks (10 ml media/flask), and then transferred to T75 flasks with an additional 15 ml of fresh media. When the cells reached confluence (typically after 3 - 6 weeks), another 25 ml of media was added, for a total of 50 ml. The cells were harvested 24 hours after adding media.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Harvested lymphoblast cell lines were pelleted by centrifugation at 1200 RPM at room temperature and washed twice with PBS buffer and repelleted. Cell pellet was suspended in 2 ml of Trizol, divided into 4 aliquots, and kept at -80 C. An aliquot of the lymphoblast-Trizol suspension was thawed and RNA was purified using the Promega SV Total RNA Isolation kit and resuspended in RNAse-free water.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was labeled at the Dana Farber Cancer Institute Microarray Core Facility using their standard protocol detailed below. 1. RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. 2. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. 3. The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. 4. The purified cRNA is fragmented in order to facilitate the subsequent hybridization step.
| | Sample_hyb_protocol | RNA was further processed at the Dana Farber Cancer Institute Microarray Core Facility using their standard protocol detailed below. 1. The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. 2. The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE. 3. Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.
| | Sample_scan_protocol | Affymetrix Microarray Suite 5.0 was used as scanning software. The target mRNA from the cell sample of interest is fragmented, fluorescently labeled, and washed over the array. Ideally, the components of the target mRNA sample will specifically hybridize to the intended PM strand. The MM strand serves as a control for non-specific cross-hybridization. The fluorescence levels at each PM and MM are then measured using a scanning microscope. MAS software outputs detected fluorescence levels at each probe. When the scanning microscope reads fluorescence activity, it dissects each probe cell (that is, each individual PM and MM cell) into a 6x6 square of pixels, and records the fluorescence levels at each pixel in a file with extension .DAT. To summarize the fluorescence at each cell, MAS ignores the 20 border pixels and returns the 75th percentile fluorescence level of the remaining 16 pixels as the Average Intensity of the probe cell, and records these values in the .CEL file.
| | Sample_data_processing | Raw data reflecting hybridization intensities, from individual probes of 25 different chips were provided as Microarray Suite (MAS) 5.0 experiment data files: .CHP, .TXT, .RPT, .EXP, .CEL (the .TXT and .CEL files are linked below as supplementary files), and were normalised using d-Chip. Background information is provided on the website: http://biosun1.harvard.edu/complab/dchip/normalizing%20arrays.htm The normalized data were extracted into a Microsoft Excel file and hybridization intensities from all probes of the affected patients in individual families were compared to all of the other samples. Significance in multiplex families was tested using a one-tailed Student’s t-test assuming unequal variance, a Bonferroni correction and P-value < 0.05. In families with only one available patient, the transcript in that patient had to have a hybridization signal more than two standard deviations below the mean hybridization intensity in all other patients.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Dyonne,T.,Hartong
| | Sample_contact_email | d.t.hartong@ohk.umcg.nl
| | Sample_contact_laboratory | Ocular Molecular Genetics Institute
| | Sample_contact_department | Massachusetts Eye and Ear Infirmary
| | Sample_contact_institute | Harvard Medical School
| | Sample_contact_address | 243 Charles Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | MA 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305067/suppl/GSM305067.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305067/suppl/GSM305067.TXT.gz
| | Sample_series_id | GSE12086
| | Sample_data_row_count | 54613
| | |
|
GSM305068 | GPL570 |
|
lymphoblast_Control_Usher_184-137
|
Lymphoblast cell line from transformed lymphocytes.
|
human_female_Usher syndrome_transformed lymphocyte
|
n/a
|
| Sample_geo_accession | GSM305068
| | Sample_status | Public on Jul 14 2008
| | Sample_submission_date | Jul 11 2008
| | Sample_last_update_date | Jul 14 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | none
| | Sample_growth_protocol_ch1 | Lymphoblasts were immortalized and grown at the Harvard Partners Center for Genetics and Genomics. Prior to harvesting for mRNA isolation, cells were grown to confluence in T25 flasks (10 ml media/flask), and then transferred to T75 flasks with an additional 15 ml of fresh media. When the cells reached confluence (typically after 3 - 6 weeks), another 25 ml of media was added, for a total of 50 ml. The cells were harvested 24 hours after adding media.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Harvested lymphoblast cell lines were pelleted by centrifugation at 1200 RPM at room temperature and washed twice with PBS buffer and repelleted. Cell pellet was suspended in 2 ml of Trizol, divided into 4 aliquots, and kept at -80 C. An aliquot of the lymphoblast-Trizol suspension was thawed and RNA was purified using the Promega SV Total RNA Isolation kit and resuspended in RNAse-free water.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was labeled at the Dana Farber Cancer Institute Microarray Core Facility using their standard protocol detailed below. 1. RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. 2. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. 3. The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. 4. The purified cRNA is fragmented in order to facilitate the subsequent hybridization step.
| | Sample_hyb_protocol | RNA was further processed at the Dana Farber Cancer Institute Microarray Core Facility using their standard protocol detailed below. 1. The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. 2. The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE. 3. Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.
| | Sample_scan_protocol | Affymetrix Microarray Suite 5.0 was used as scanning software. The target mRNA from the cell sample of interest is fragmented, fluorescently labeled, and washed over the array. Ideally, the components of the target mRNA sample will specifically hybridize to the intended PM strand. The MM strand serves as a control for non-specific cross-hybridization. The fluorescence levels at each PM and MM are then measured using a scanning microscope. MAS software outputs detected fluorescence levels at each probe. When the scanning microscope reads fluorescence activity, it dissects each probe cell (that is, each individual PM and MM cell) into a 6x6 square of pixels, and records the fluorescence levels at each pixel in a file with extension .DAT. To summarize the fluorescence at each cell, MAS ignores the 20 border pixels and returns the 75th percentile fluorescence level of the remaining 16 pixels as the Average Intensity of the probe cell, and records these values in the .CEL file.
| | Sample_data_processing | Raw data reflecting hybridization intensities, from individual probes of 25 different chips were provided as Microarray Suite (MAS) 5.0 experiment data files: .CHP, .TXT, .RPT, .EXP, .CEL (the .TXT and .CEL files are linked below as supplementary files), and were normalised using d-Chip. Background information is provided on the website: http://biosun1.harvard.edu/complab/dchip/normalizing%20arrays.htm The normalized data were extracted into a Microsoft Excel file and hybridization intensities from all probes of the affected patients in individual families were compared to all of the other samples. Significance in multiplex families was tested using a one-tailed Student’s t-test assuming unequal variance, a Bonferroni correction and P-value < 0.05. In families with only one available patient, the transcript in that patient had to have a hybridization signal more than two standard deviations below the mean hybridization intensity in all other patients.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Dyonne,T.,Hartong
| | Sample_contact_email | d.t.hartong@ohk.umcg.nl
| | Sample_contact_laboratory | Ocular Molecular Genetics Institute
| | Sample_contact_department | Massachusetts Eye and Ear Infirmary
| | Sample_contact_institute | Harvard Medical School
| | Sample_contact_address | 243 Charles Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | MA 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305068/suppl/GSM305068.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305068/suppl/GSM305068.TXT.gz
| | Sample_series_id | GSE12086
| | Sample_data_row_count | 54613
| | |
|
GSM305069 | GPL570 |
|
lymphoblast_Control_Usher_184-135
|
Lymphoblast cell line from transformed lymphocytes.
|
human_female_Usher syndrome_transformed lymphocyte
|
n/a
|
| Sample_geo_accession | GSM305069
| | Sample_status | Public on Jul 14 2008
| | Sample_submission_date | Jul 11 2008
| | Sample_last_update_date | Jul 14 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | none
| | Sample_growth_protocol_ch1 | Lymphoblasts were immortalized and grown at the Harvard Partners Center for Genetics and Genomics. Prior to harvesting for mRNA isolation, cells were grown to confluence in T25 flasks (10 ml media/flask), and then transferred to T75 flasks with an additional 15 ml of fresh media. When the cells reached confluence (typically after 3 - 6 weeks), another 25 ml of media was added, for a total of 50 ml. The cells were harvested 24 hours after adding media.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Harvested lymphoblast cell lines were pelleted by centrifugation at 1200 RPM at room temperature and washed twice with PBS buffer and repelleted. Cell pellet was suspended in 2 ml of Trizol, divided into 4 aliquots, and kept at -80 C. An aliquot of the lymphoblast-Trizol suspension was thawed and RNA was purified using the Promega SV Total RNA Isolation kit and resuspended in RNAse-free water.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was labeled at the Dana Farber Cancer Institute Microarray Core Facility using their standard protocol detailed below. 1. RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. 2. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. 3. The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. 4. The purified cRNA is fragmented in order to facilitate the subsequent hybridization step.
| | Sample_hyb_protocol | RNA was further processed at the Dana Farber Cancer Institute Microarray Core Facility using their standard protocol detailed below. 1. The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. 2. The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE. 3. Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.
| | Sample_scan_protocol | Affymetrix Microarray Suite 5.0 was used as scanning software. The target mRNA from the cell sample of interest is fragmented, fluorescently labeled, and washed over the array. Ideally, the components of the target mRNA sample will specifically hybridize to the intended PM strand. The MM strand serves as a control for non-specific cross-hybridization. The fluorescence levels at each PM and MM are then measured using a scanning microscope. MAS software outputs detected fluorescence levels at each probe. When the scanning microscope reads fluorescence activity, it dissects each probe cell (that is, each individual PM and MM cell) into a 6x6 square of pixels, and records the fluorescence levels at each pixel in a file with extension .DAT. To summarize the fluorescence at each cell, MAS ignores the 20 border pixels and returns the 75th percentile fluorescence level of the remaining 16 pixels as the Average Intensity of the probe cell, and records these values in the .CEL file.
| | Sample_data_processing | Raw data reflecting hybridization intensities, from individual probes of 25 different chips were provided as Microarray Suite (MAS) 5.0 experiment data files: .CHP, .TXT, .RPT, .EXP, .CEL (the .TXT and .CEL files are linked below as supplementary files), and were normalised using d-Chip. Background information is provided on the website: http://biosun1.harvard.edu/complab/dchip/normalizing%20arrays.htm The normalized data were extracted into a Microsoft Excel file and hybridization intensities from all probes of the affected patients in individual families were compared to all of the other samples. Significance in multiplex families was tested using a one-tailed Student’s t-test assuming unequal variance, a Bonferroni correction and P-value < 0.05. In families with only one available patient, the transcript in that patient had to have a hybridization signal more than two standard deviations below the mean hybridization intensity in all other patients.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Dyonne,T.,Hartong
| | Sample_contact_email | d.t.hartong@ohk.umcg.nl
| | Sample_contact_laboratory | Ocular Molecular Genetics Institute
| | Sample_contact_department | Massachusetts Eye and Ear Infirmary
| | Sample_contact_institute | Harvard Medical School
| | Sample_contact_address | 243 Charles Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | MA 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305069/suppl/GSM305069.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305069/suppl/GSM305069.TXT.gz
| | Sample_series_id | GSE12086
| | Sample_data_row_count | 54613
| | |
|
GSM305070 | GPL570 |
|
lymphoblast_Control_rhodopsin_001-204
|
Lymphoblast cell line from transformed lymphocytes.
|
human_male_dominant retinitis pigmentosa_transformed lymphocyte
|
n/a
|
| Sample_geo_accession | GSM305070
| | Sample_status | Public on Jul 14 2008
| | Sample_submission_date | Jul 11 2008
| | Sample_last_update_date | Jul 14 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | none
| | Sample_growth_protocol_ch1 | Lymphoblasts were immortalized and grown at the Harvard Partners Center for Genetics and Genomics. Prior to harvesting for mRNA isolation, cells were grown to confluence in T25 flasks (10 ml media/flask), and then transferred to T75 flasks with an additional 15 ml of fresh media. When the cells reached confluence (typically after 3 - 6 weeks), another 25 ml of media was added, for a total of 50 ml. The cells were harvested 24 hours after adding media.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Harvested lymphoblast cell lines were pelleted by centrifugation at 1200 RPM at room temperature and washed twice with PBS buffer and repelleted. Cell pellet was suspended in 2 ml of Trizol, divided into 4 aliquots, and kept at -80 C. An aliquot of the lymphoblast-Trizol suspension was thawed and RNA was purified using the Promega SV Total RNA Isolation kit and resuspended in RNAse-free water.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was labeled at the Dana Farber Cancer Institute Microarray Core Facility using their standard protocol detailed below. 1. RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. 2. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. 3. The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. 4. The purified cRNA is fragmented in order to facilitate the subsequent hybridization step.
| | Sample_hyb_protocol | RNA was further processed at the Dana Farber Cancer Institute Microarray Core Facility using their standard protocol detailed below. 1. The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. 2. The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE. 3. Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.
| | Sample_scan_protocol | Affymetrix Microarray Suite 5.0 was used as scanning software. The target mRNA from the cell sample of interest is fragmented, fluorescently labeled, and washed over the array. Ideally, the components of the target mRNA sample will specifically hybridize to the intended PM strand. The MM strand serves as a control for non-specific cross-hybridization. The fluorescence levels at each PM and MM are then measured using a scanning microscope. MAS software outputs detected fluorescence levels at each probe. When the scanning microscope reads fluorescence activity, it dissects each probe cell (that is, each individual PM and MM cell) into a 6x6 square of pixels, and records the fluorescence levels at each pixel in a file with extension .DAT. To summarize the fluorescence at each cell, MAS ignores the 20 border pixels and returns the 75th percentile fluorescence level of the remaining 16 pixels as the Average Intensity of the probe cell, and records these values in the .CEL file.
| | Sample_data_processing | Raw data reflecting hybridization intensities, from individual probes of 25 different chips were provided as Microarray Suite (MAS) 5.0 experiment data files: .CHP, .TXT, .RPT, .EXP, .CEL (the .TXT and .CEL files are linked below as supplementary files), and were normalised using d-Chip. Background information is provided on the website: http://biosun1.harvard.edu/complab/dchip/normalizing%20arrays.htm The normalized data were extracted into a Microsoft Excel file and hybridization intensities from all probes of the affected patients in individual families were compared to all of the other samples. Significance in multiplex families was tested using a one-tailed Student’s t-test assuming unequal variance, a Bonferroni correction and P-value < 0.05. In families with only one available patient, the transcript in that patient had to have a hybridization signal more than two standard deviations below the mean hybridization intensity in all other patients.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Dyonne,T.,Hartong
| | Sample_contact_email | d.t.hartong@ohk.umcg.nl
| | Sample_contact_laboratory | Ocular Molecular Genetics Institute
| | Sample_contact_department | Massachusetts Eye and Ear Infirmary
| | Sample_contact_institute | Harvard Medical School
| | Sample_contact_address | 243 Charles Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | MA 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305070/suppl/GSM305070.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305070/suppl/GSM305070.TXT.gz
| | Sample_series_id | GSE12086
| | Sample_data_row_count | 54613
| | |
|
GSM305071 | GPL570 |
|
lymphoblast_Control_normal_226-1823
|
Lymphoblast cell line from transformed lymphocytes.
|
human_female_unaffected_transformed lymphocyte
|
n/a
|
| Sample_geo_accession | GSM305071
| | Sample_status | Public on Jul 14 2008
| | Sample_submission_date | Jul 11 2008
| | Sample_last_update_date | Jul 14 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | none
| | Sample_growth_protocol_ch1 | Lymphoblasts were immortalized and grown at the Harvard Partners Center for Genetics and Genomics. Prior to harvesting for mRNA isolation, cells were grown to confluence in T25 flasks (10 ml media/flask), and then transferred to T75 flasks with an additional 15 ml of fresh media. When the cells reached confluence (typically after 3 - 6 weeks), another 25 ml of media was added, for a total of 50 ml. The cells were harvested 24 hours after adding media.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Harvested lymphoblast cell lines were pelleted by centrifugation at 1200 RPM at room temperature and washed twice with PBS buffer and repelleted. Cell pellet was suspended in 2 ml of Trizol, divided into 4 aliquots, and kept at -80 C. An aliquot of the lymphoblast-Trizol suspension was thawed and RNA was purified using the Promega SV Total RNA Isolation kit and resuspended in RNAse-free water.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was labeled at the Dana Farber Cancer Institute Microarray Core Facility using their standard protocol detailed below. 1. RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. 2. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. 3. The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. 4. The purified cRNA is fragmented in order to facilitate the subsequent hybridization step.
| | Sample_hyb_protocol | RNA was further processed at the Dana Farber Cancer Institute Microarray Core Facility using their standard protocol detailed below. 1. The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. 2. The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE. 3. Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.
| | Sample_scan_protocol | Affymetrix Microarray Suite 5.0 was used as scanning software. The target mRNA from the cell sample of interest is fragmented, fluorescently labeled, and washed over the array. Ideally, the components of the target mRNA sample will specifically hybridize to the intended PM strand. The MM strand serves as a control for non-specific cross-hybridization. The fluorescence levels at each PM and MM are then measured using a scanning microscope. MAS software outputs detected fluorescence levels at each probe. When the scanning microscope reads fluorescence activity, it dissects each probe cell (that is, each individual PM and MM cell) into a 6x6 square of pixels, and records the fluorescence levels at each pixel in a file with extension .DAT. To summarize the fluorescence at each cell, MAS ignores the 20 border pixels and returns the 75th percentile fluorescence level of the remaining 16 pixels as the Average Intensity of the probe cell, and records these values in the .CEL file.
| | Sample_data_processing | Raw data reflecting hybridization intensities, from individual probes of 25 different chips were provided as Microarray Suite (MAS) 5.0 experiment data files: .CHP, .TXT, .RPT, .EXP, .CEL (the .TXT and .CEL files are linked below as supplementary files), and were normalised using d-Chip. Background information is provided on the website: http://biosun1.harvard.edu/complab/dchip/normalizing%20arrays.htm The normalized data were extracted into a Microsoft Excel file and hybridization intensities from all probes of the affected patients in individual families were compared to all of the other samples. Significance in multiplex families was tested using a one-tailed Student’s t-test assuming unequal variance, a Bonferroni correction and P-value < 0.05. In families with only one available patient, the transcript in that patient had to have a hybridization signal more than two standard deviations below the mean hybridization intensity in all other patients.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Dyonne,T.,Hartong
| | Sample_contact_email | d.t.hartong@ohk.umcg.nl
| | Sample_contact_laboratory | Ocular Molecular Genetics Institute
| | Sample_contact_department | Massachusetts Eye and Ear Infirmary
| | Sample_contact_institute | Harvard Medical School
| | Sample_contact_address | 243 Charles Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | MA 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305071/suppl/GSM305071.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305071/suppl/GSM305071.TXT.gz
| | Sample_series_id | GSE12086
| | Sample_data_row_count | 54613
| | |
|
| |
| |
Make groups for comparisons |
(2 groups will be compared at a time) |
|
| Select GSMs and click on "Add groups" |
Enter the group name here: |
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